A charter plane holding three of the five Americans released by Iran landed in Germany Sunday afternoon, as one of the freed captives mysteriously chose to remain.

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U.S. officials said Nosratollah Khosravi-Roodsari decided to stay in Iran. "It's his free determination," one White House official told reporters. "We don't make that judgment."

Khosravi-Roodsari's case remains a total mystery.

It is unclear why he was imprisoned, how long he was in captivity, or why he decided to stay.

As for the other captives, friends and family members were overwhelmed with joy.

That includes Washington Post publisher Frederick Ryan, who has long lobbied for reporter Jason Rezaian.

"We are relieved that this 545-day nightmare for Jason and his family is finally over," he said in a statement.

The others on the flight were former U.S. Marine Amir Hekmati and pastor Saeed Abedini.

People walk off a plane carrying three Iranian-Americans, who left Tehran under a prisoner swap, after it landed at Cointrin airport in Geneva, Switzerland Sunday. (DENIS BALIBOUSE/REUTERS)

Hekmati's family said "it is hard to put into words what our family feels right now."

Earlier on Sunday, the three Americans landed in Geneva aboard a Swiss air force plane.

U.S. officials had said Saturday that the released prisoners would be taken to a U.S. military hospital for medical treatment. The hospital is near the U.S. military's Ranstein Air Base.

As part of the deal, the U.S. pardoned or dropped the charges against seven Iranians in a prisoner swap for the four Americans held by Iran.

The agreement also called for the lifting of stiff economic sanctions now that the Islamic Republic has met a critical benchmark to pull back its nuclear program.

Secretary of State John Kerry said U.S. officials hashed out the prisoner exchange over 11 or 12 meetings with the Iranians. At times, the Americans thought a deal was set, only to get stuck on the details.

After almost constant conversation over the last few days, they finally did settle it.

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Kerry said the nuclear agreement provided the key impetus.

Jason Rezaian, an Iranian-American correspondent for the Washington Post, was released from an Iranian prison. (STR/EPA)

Just before Iran's foreign minister, Mohammad Javad Zarif, announced the July 14 accord with his European Union counterpart, Kerry again raised the issue of the detained Americans.

A photograph of him speaking with Zarif and Iranian President Hasan Rouhani's brother, Hossein Fereydoun, captured the moment.

Things progressed significantly by a November meeting in Vienna on Syria's civil war, when, for the first time, Iran was included in the discussions. Kerry and Zarif met on the sidelines of the talks to discuss the prisoners.

"We actually shook hands thinking we had an agreement," Kerry said. "I thought it was done."

But the deal bogged down in Tehran and never went through. "So we went back to work," Kerry said.

He described the negotiations as difficult, especially as the Iranians made what he said were unacceptable demands. Kerry said the United States made it clear that it would not release a hardened criminal such as an accused murderer or someone with a narcotics record.

"For a long time, this didn't move because of the people they were asking for," Kerry recalled. "We said, 'No, and no, and no."'

"And believe me, it's hard when somebody says to you, 'Hey, you give us this guy, we let them all out.' And you have to say no. And you know you're keeping people in a not very nice place for the next whatever number of months," he said.

"But there have to be an enforcement of our principles and our standards here. And in the end, we came out in the right place on that."

More progress was made by Kerry's meeting with Zarif on Dec. 18 in New York. By then, American and Iranian teams in Geneva were working hard on the details of the swap.

The U.S. was prepared to release individuals who violated nuclear-related sanctions on Iran, Kerry said. By Saturday night, those penalties were no longer in effect. "In the end, the president made the call," he said.

Talking to reporters in his plane after landing Sunday morning at Andrews Air Force Base, Kerry said he had hoped to meet the returning Americans in Switzerland.

But after the nuclear talks moved to Vienna and dragged on, he decided to send the lead negotiator on the matter, Brett McGurk, and State Department aide Patrick Kennedy, to await the Americans' arrival.

One of the last hiccups that delayed the Americans' departure was an Iranian military official's misunderstanding about Rezaian's wife and mother joining him on the flight. After Kerry spoke to Zarif, that problem was solved. Permission was granted.

But the various administrative holdups meant that the Swiss crew set to fly the plane ran into a mandatory crew rest. That set back takeoff several hours.

Kerry said the prisoner swap and almost simultaneous implementation of the nuclear deal raise the prospects of increased U.S.-Iranian cooperation on other matters. Zarif, Kerry said, made it clear that if they got the two tasks done, "there are ways to try to translate this and hopefully be constructive in other things. He specifically said Syria and Yemen."

Amir Hekmati, a former U.S. Marine held in Iran over the past two years on accusations of spying for the CIA, was freed in a prisoner exchange Sunday. (Uncredited/AP)

"I put a big, 'Who knows?"' on that, Kerry said, but expressed hope.

Kerry said he would remain at work on other Americans still being held in Iran.

The exchange did not cover Siamak Namazi, an Iranian-American businessman who advocated better ties between Iran and the U.S. and who reportedly was arrested in October, or former FBI agent Robert Levinson, who disappeared in Iran in 2007 on an unauthorized CIA mission.

Asked if Levinson was dead or alive, Kerry said, "We have no idea."

The exchange eases a leading irritant as the two countries gingerly explore prospects for a smoother relationship after decades of hostility - even as they remain sharply at odds on other fronts.

A fifth American, student Matthew Trevithick was released independently of the larger swap, and already had headed home.